devicely 0.2.5

Read multiple signals from different sources.

Documentation

https://hpi-dhc.github.io/devicely/

Description

Package containing readers for reading data from different devices. You can also timeshift the data to a specified interval and write the data back.

For a sample dataset go to: https://doi.org/10.6084/m9.figshare.12646217

So far, we have integrated:

Empatica E4 (Firmware 2.1.0.4911)

Link

Biovotion Everion (Firmware 03.06)

Link

1-lead ECG monitor Faros^TM 180 from Bittium (Firmware 3.5.1)

Link

Spacelabs (SL 90217)

Link

Tags (obtained from the app: TimeStamp for Android Version 1.36)

Link

Shimmer Consensys GSR (Shimmer3 GSR Development Kit)

Link

Basic Usage

To use the package, after cloning this repository:

pip install .

Then:

import devicely

Example

shift = pd.Timedelta(15,unit='d')

Tags

Reading Tags from the TimeStamp App

Timeshifting and Writing them back

tags = devicely.TagReader(tags_path)
tags.data.head()

tags.timeshift(shift)
tags.data.head()

tags.write(join(write_path, 'tags.csv'))

Empatica

Reading Empatica E4 Data

Timeshifting and Writing them back

empatica = devicely.EmpaticaReader(empatica_path)
empatica.data.head()

empatica.timeshift(shift)
empatica.data.head()

empatica.write(join(write_path, 'Empatica'))

Faros

Reading Bittium Faros 180 Data

Timeshifting and Writing them back

faros = devicely.FarosReader(faros_path)
faros.data.head()

faros.timeshift(shift)
faros.data.head()

faros.write(join(write_path, 'faros.csv'))

Biovotion

Reading Biovotion Everion Data

Timeshifting and Writing them back

• The reader method detects automatically if the sensors file is present or not.

everion = devicely.EverionReader(everion_path)
everion.data.head()

everion.timeshift(shift)
everion.data.head()

everion.write(join(write_path, 'Everion'))

Spacelabs

Reading Spacelabs Data

Timeshifting, Deidentifying and Writing them back

• The method deidentify generates a random subject id or you can specify one (e.g. 001)

• The method drop_EB will drop lines with an EB error

• The method set_window will create a timedelta window around the blood pressure measurement (e.g. 30 secs)

  • The type of window is defined by: bfill (before the start of the measurement), bffil (half before and half after) of ffill (after the start of the measurement)

spacelabs = devicely.SpacelabsReader(spacelabs_path)
spacelabs.data.head()

spacelabs.timeshift(shift)
spacelabs.deidentify('001')
spacelabs.drop_EB()
spacelabs.data.head()

spacelabs.set_window(timedelta(seconds=30), 'bfill')
spacelabs.data.head()

spacelabs.write(join(write_path, 'spacelabs.abp'))

Shimmer

Reading Shimmer Consensys GSR (Shimmer3 GSR Development Kit)

Timeshifting and Writing them back

• Please define your csv delimiter (e.g. , ; \t) in the reader method

shimmer_plus = devicely.ShimmerPlusReader(shimmer_file_path, delimiter=';')
shimmer_plus.data.head()

shimmer_plus.timeshift(shift)
shimmer_plus.data.head()

shimmer_plus.write(join(write_path, 'shimmer_plus.csv'))

To run a notebook with examples:

pipenv install
pipenv shell
pipenv run jupyter notebook

And open example.ipynb

Contributors

* Ariane Sasso
* Arpita Kappattanavar
* Bjarne Pfitzner
* Felix Musmann
* Jost Morgenstern
* Lin Zhou
* Pascal Hecker